Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1610 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0217059437 sf0217053567 2 17059437 3.17E-30 6.18E-18
vg0217069340 sf0217063470 2 17069340 1.50E-29 4.25E-18
vg0216978452 sf0216972582 2 16978452 1.39E-28 1.78E-17
vg0217596613 sf0217590743 2 17596613 5.89E-13 3.14E-07
vg1220336354 sf1220307796 12 20336354 6.72E-13 5.12E-06
vg1216728475 sf1216722429 12 16728475 1.32E-12 NA
vg0216350599 sf0216344729 2 16350599 1.79E-12 4.45E-07
vg0217596619 sf0217590749 2 17596619 2.69E-12 4.93E-07
vg0212591710 sf0212591706 2 12591710 7.93E-12 3.93E-06
vg0216350616 sf0216344746 2 16350616 1.91E-11 1.53E-06
vg0218790628 sf0218784759 2 18790628 2.48E-11 4.14E-06
vg1003674168 sf1003673145 10 3674168 1.34E-10 5.34E-08
vg0217807070 sf0217801201 2 17807070 1.83E-10 1.75E-06
vg0216133151 sf0216127281 2 16133151 5.99E-10 3.61E-06
vg0215550979 sf0215545109 2 15550979 7.22E-10 4.71E-07
vg0211892318 sf0211892314 2 11892318 6.22E-09 4.31E-06
vg0421568928 sf0421396978 4 21568928 9.86E-07 1.45E-06
vg1210467503 sf1210464916 12 10467503 2.88E-06 3.47E-06
vg0217027791 sf0217021921 2 17027791 NA 3.76E-06